LAMMPS (18 Jun 2019) OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:88) using 1 OpenMP thread(s) per MPI task clear OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:88) using 1 OpenMP thread(s) per MPI task # The units we assume we'll use. The kim-lammps-preprocessor # may swap this line out if running against a Simulator Model # whose units are not 'metal' units metal # Variables that can be adjusted by kim-lammps-preprocessor# to switch unit sets for Simulator Models variable _u_distance equal 1.0 variable _u_energy equal 1.0 variable _u_mass equal 1.0 variable _u_pressure equal 1.0 dimension 3 boundary p p p # This line may be swapped out by kim-lammps-preprocessor if # running against a Simulator Model whose atom_style is not # 'atomic' atom_style atomic # Adjust input variables for possible units changes with Simulator Models variable lattice_constant_converted equal 3.987558534741402*${_u_distance} variable lattice_constant_converted equal 3.987558534741402*1 variable xmin_converted equal 0.0*${_u_distance} variable xmin_converted equal 0.0*1 variable xmax_converted equal 5.639259360587877*${_u_distance} variable xmax_converted equal 5.639259360587877*1 variable ymin_converted equal -45.118062443237754*${_u_distance} variable ymin_converted equal -45.118062443237754*1 variable ymax_converted equal 45.118062443237754*${_u_distance} variable ymax_converted equal 45.118062443237754*1 variable zmin_converted equal 0.0*${_u_distance} variable zmin_converted equal 0.0*1 variable zmax_converted equal 3.987558534741402*${_u_distance} variable zmax_converted equal 3.987558534741402*1 lattice fcc ${lattice_constant_converted} lattice fcc 3.9875585347414 Lattice spacing in x,y,z = 3.98756 3.98756 3.98756 region whole block ${xmin_converted} ${xmax_converted} ${ymin_converted} ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 ${xmax_converted} ${ymin_converted} ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 5.63925936058788 ${ymin_converted} ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 5.63925936058788 -45.1180624432378 ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 5.63925936058788 -45.1180624432378 45.1180624432378 ${zmin_converted} ${zmax_converted} units box region whole block 0 5.63925936058788 -45.1180624432378 45.1180624432378 0 ${zmax_converted} units box region whole block 0 5.63925936058788 -45.1180624432378 45.1180624432378 0 3.9875585347414 units box create_box 2 whole Created orthogonal box = (0 -45.1181 0) to (5.63926 45.1181 3.98756) 1 by 1 by 1 MPI processor grid region upper block INF INF 0.0 ${ymax_converted} INF INF units box region upper block INF INF 0.0 45.1180624432378 INF INF units box lattice fcc ${lattice_constant_converted} orient x 1 -1 0 orient y 1 1 0 orient z 0 0 1 lattice fcc 3.9875585347414 orient x 1 -1 0 orient y 1 1 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.63926 5.63926 3.98756 create_atoms 1 region upper Created 66 atoms create_atoms CPU = 0.000189066 secs group upper type 1 66 atoms in group upper mass 1 26.981538*${_u_mass} mass 1 26.981538*1 displace_atoms upper move 0.6363961030678927 0 0.3333333333333333 units lattice region lower block INF INF ${ymin_converted} 0.0 INF INF units box region lower block INF INF -45.1180624432378 0.0 INF INF units box lattice fcc ${lattice_constant_converted} orient x 1 1 0 orient y -1 1 0 orient z 0 0 1 lattice fcc 3.9875585347414 orient x 1 1 0 orient y -1 1 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.63926 5.63926 3.98756 create_atoms 2 region lower Created 66 atoms create_atoms CPU = 6.41346e-05 secs group lower type 2 66 atoms in group lower displace_atoms lower move -0.6363961030678927 0 -0.3333333333333333 units lattice mass 2 26.981538*${_u_mass} mass 2 26.981538*1 pair_style kim EAM_Dynamo_JacobsenNorskovPuska_1987_Al__MO_411692133366_000 pair_coeff * * Al Al variable neigh_skin_converted equal 2.0*${_u_distance} variable neigh_skin_converted equal 2.0*1 neighbor ${neigh_skin_converted} bin neighbor 2 bin neigh_modify delay 10 check yes variable delete_distance equal 0.5*${lattice_constant_converted} variable delete_distance equal 0.5*3.9875585347414 delete_atoms overlap ${delete_distance} all all delete_atoms overlap 1.9937792673707 all all Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 8 ghost atom cutoff = 8 binsize = 4, bins = 2 23 1 2 neighbor lists, perpetual/occasional/extra = 1 1 0 (1) command delete_atoms, occasional attributes: full, newton on pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (2) pair kim, perpetual attributes: full, newton off, cut 8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 8 atoms, new total = 124 min_style cg minimize 1e-15 1e-15 5000 10000 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:168) Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 8 ghost atom cutoff = 8 binsize = 4, bins = 2 23 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 4.428 | 4.428 | 4.428 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -415.94435 0 -415.94435 -5615.3936 142 0 -419.2341 0 -419.2341 -27057.295 Loop time of 0.0886121 on 1 procs for 142 steps with 124 atoms 90.3% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -415.944347168 -419.234095432 -419.234095432 Force two-norm initial, final = 1.17774 1.12954e-06 Force max component initial, final = 0.397718 1.62216e-07 Final line search alpha, max atom move = 1 1.62216e-07 Iterations, force evaluations = 142 277 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.084247 | 0.084247 | 0.084247 | 0.0 | 95.07 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0033262 | 0.0033262 | 0.0033262 | 0.0 | 3.75 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001039 | | | 1.17 Nlocal: 124 ave 124 max 124 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2756 ave 2756 max 2756 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 16872 ave 16872 max 16872 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 16872 Ave neighs/atom = 136.065 Neighbor list builds = 0 Dangerous builds = 0 fix 1 all box/relax x 0.0 z 0.0 couple none vmax 0.001 minimize 1.0e-25 1.0e-25 1000 10000 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:168) Per MPI rank memory allocation (min/avg/max) = 4.428 | 4.428 | 4.428 Mbytes Step Temp E_pair E_mol TotEng Press Volume 142 0 -419.2341 0 -419.2341 -27057.295 2029.1286 829 0 -419.66448 0 -419.66448 -6227.9373 1980.5417 Loop time of 0.681017 on 1 procs for 687 steps with 124 atoms 98.4% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -419.234095432 -419.664475082 -419.664475082 Force two-norm initial, final = 37.9576 2.74287e-11 Force max component initial, final = 32.2627 2.1932e-11 Final line search alpha, max atom move = 1 2.1932e-11 Iterations, force evaluations = 687 1344 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.60286 | 0.60286 | 0.60286 | 0.0 | 88.52 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.020329 | 0.020329 | 0.020329 | 0.0 | 2.99 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.05783 | | | 8.49 Nlocal: 124 ave 124 max 124 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2756 ave 2756 max 2756 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 16864 ave 16864 max 16864 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 16864 Ave neighs/atom = 136 Neighbor list builds = 0 Dangerous builds = 0 unfix 1 # Variables used to rescale the positions and energies so that the quantities # in the dumpfile are in the original metal units (angstrom and eV) # even if we're running with a Simulator Model that uses different units variable pe_metal equal "c_thermo_pe/v__u_energy" variable lx_metal equal lx/${_u_distance} variable lx_metal equal lx/1 variable ly_metal equal ly/${_u_distance} variable ly_metal equal ly/1 variable lz_metal equal lz/${_u_distance} variable lz_metal equal lz/1 variable press_metal equal "c_thermo_press/v__u_pressure" variable pxx_metal equal pxx/${_u_pressure} variable pxx_metal equal pxx/1 variable pyy_metal equal pyy/${_u_pressure} variable pyy_metal equal pyy/1 variable pzz_metal equal pzz/${_u_pressure} variable pzz_metal equal pzz/1 variable mass_metal atom mass/${_u_mass} variable mass_metal atom mass/1 compute csym all centro/atom fcc compute particle_eng all pe/atom compute particle_engsum all reduce sum c_particle_eng compute csymsum all reduce sum c_csym compute distance all pair/local dist compute mindist all reduce min c_distance # Isolated atom energy in eV (no unit conversion necessary) variable isolated_atom_energy equal -1.81000000000002 variable particle_eng_metal atom "c_particle_eng/v__u_energy - v_isolated_atom_energy" variable csym_metal atom c_csym/(${_u_distance}*${_u_distance}) variable csym_metal atom c_csym/(1*${_u_distance}) variable csym_metal atom c_csym/(1*1) variable csymsum_metal equal c_csymsum/(${_u_distance}*${_u_distance}) variable csymsum_metal equal c_csymsum/(1*${_u_distance}) variable csymsum_metal equal c_csymsum/(1*1) variable mindist_metal equal c_mindist/${_u_distance} variable mindist_metal equal c_mindist/1 reset_timestep 0 run 0 WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 8 ghost atom cutoff = 8 binsize = 4, bins = 2 23 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (2) compute centro/atom, occasional attributes: full, newton on pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (3) compute pair/local, occasional attributes: half, newton on pair build: half/bin/atomonly/newton stencil: half/bin/3d/newton bin: standard Per MPI rank memory allocation (min/avg/max) = 4.566 | 4.566 | 4.566 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -419.66448 0 -419.66448 -6227.9373 Loop time of 9.53674e-07 on 1 procs for 0 steps with 124 atoms 0.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0 | 0 | 0 | 0.0 | 0.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 9.537e-07 | | |100.00 Nlocal: 124 ave 124 max 124 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2756 ave 2756 max 2756 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 16864 ave 16864 max 16864 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 16864 Ave neighs/atom = 136 Neighbor list builds = 0 Dangerous builds = 0 thermo 0 thermo_style custom step v_pe_metal c_particle_engsum v_lx_metal v_ly_metal v_lz_metal press v_press_metal v_pxx_metal v_pyy_metal v_pzz_metal v_mindist_metal v_csymsum_metal run 0 WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) Per MPI rank memory allocation (min/avg/max) = 4.566 | 4.566 | 4.566 Mbytes Step v_pe_metal c_particle_engsum v_lx_metal v_ly_metal v_lz_metal Press v_press_metal v_pxx_metal v_pyy_metal v_pzz_metal v_mindist_metal v_csymsum_metal 0 -419.66448 -419.66448 5.6747646 90.236125 3.867726 -6227.9373 -6227.9373 1.7853802e-08 -18683.812 3.9942969e-09 2.8054879 1.3307826e-21 Loop time of 0 on 1 procs for 0 steps with 124 atoms 0.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0 | 0 | 0 | 0.0 | 0.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0 | | | 0.00 Nlocal: 124 ave 124 max 124 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2756 ave 2756 max 2756 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 8432 ave 8432 max 8432 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 16864 ave 16864 max 16864 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 16864 Ave neighs/atom = 136 Neighbor list builds = 0 Dangerous builds = 0 variable num_atoms equal "count(all)" print "${num_atoms}" file output/dump_090.0000/numatoms.out 124 variable adjusted_pe_metal equal ${pe_metal}-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -419.664475082032-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -419.664475082032-124*${isolated_atom_energy} variable adjusted_pe_metal equal -419.664475082032-124*-1.81000000000002 print "${adjusted_pe_metal} eV" file output/dump_090.0000/energy.out -195.22447508203 eV print "${mindist_metal} Angstroms" file output/dump_090.0000/mindistance.out 2.80548786670447 Angstroms write_dump all cfg output/dump_090.0000/dump_post.cfg mass type xs ys zs id v_mass_metal v_csym_metal v_particle_eng_metal modify element Al Al print "This indicates that LAMMPS ran successfully" file output/dump_090.0000/success.out This indicates that LAMMPS ran successfully Total wall time: 0:00:00